TOMTOM

Name	Preview	Matches	List
1_e_k4me1-h1_0.558	TATGCAAATG	13	OCT_C_M00210_T, OCT1_B_M00342_T, OCT_Q6_M00795_T, IL24_5_H, nub_MA0453.1_J, OCT1_Q5_01_M00930_T, Pou2f2_3748.1_Cell08_U, Pou2f3_3986.2_Cell08_U, OCT2_01_M01368_T, POU2F3_01_M01476_T
2_e_k4me1-tro_0.552	GCCTCAGGC	2	Tcfap2e_primary_SCI09_U, AP2ALPHA_03_M01047_T
3_e_k4me1-h1_0.541	GTATGCACA	0
4_e_k4me1-tro_0.538	GATCTGGCC	0
5_e_k4me1-h1_0.536	TCATTAGCA	0
6_h_k4me1-tro_0.535	CCTAAGGG	0
7_e_k4me1-tro_0.534	CCTGGGGCCA	0
8_e_k4me1-tro_0.534	GACTTCAGA	0
9_e_k4me1-tro_0.534	CAACTTTGG	0
10_e_k4me1-tro_0.533	AAAATCTGT	0
11_e_k4me1-h1_0.533	CACGTGCAC	3	CBF1_02_M01699_T, Mycn_MA0104.1_J, Arnt_MA0004.1_J
12_e_k4me1-tro_0.529	CAAGTCCCAG	0
13_e_k4me1-tro_0.528	ATGACTCAT	18	FRA1_Q5_M01267_T, BACH2_01_M00490_T, AP1_Q4_01_M00926_T, AP1_Q6_01_M00925_T, GCN4_01_M00038_T, AP1_Q6_M00174_T, AP1_01_M00517_T, AP1_C_M00199_T, AP1_MA0099.2_J, BACH1_01_M00495_T
14_h_k4me1-tro_0.528	ACAGGTCA	4	RPS10_5_H, ZNF655_8_H, CBX7_5_H, NUP133_3_H
15_e_k4me1-h1_0.528	ATGCAGAGC	0
16_e_k4me1-h1_0.526	ATGCTATGC	0
17_e_k4me1-tro_0.526	AAACAGAACT	0
18_e_k4me1-h1_0.526	GAAAGCGAT	0
19_e_k4me1-tro_0.526	AAACAGTCTAG	0
20_e_k4me1-tro_0.525	TAGCCTCTTC	0
21_e_k4me1-h1_0.525	AACGCTAATG	0
22_e_k4me1-tro_0.524	AGAAAACTGGA	0
23_e_k4me1-tro_0.523	GACCGAACC	0
24_e_k4me1-tro_0.523	GCCAAAACC	0
25_e_k4me1-h1_0.522	GCGTGTTAA	0
26_e_k4me1-tro_0.521	ATTCCCCAG	0
27_e_k4me1-h1_0.520	ATAGCACC	0
28_e_k4me1-tro_0.519	GAGAAAGCCT	0
29_e_k4me1-h1_0.517	ACAAAACAG	0
30_e_k4me1-h1_0.516	CTAAACACCA	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	40

Summary

Alignment

Name	OCT_C_M00210_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.34924e-08
E-value	0.000185461
q-value	0.000368702
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	OCT1_B_M00342_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.39844e-07
E-value	0.00157688
q-value	0.00156745
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	OCT_Q6_M00795_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.6303e-07
E-value	0.00252091
q-value	0.00167055
Overlap	10
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	IL24_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.09202e-06
E-value	0.00611078
q-value	0.00183772
Overlap	8
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	nub_MA0453.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.50726e-06
E-value	0.00732372
q-value	0.00183772
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	OCT1_Q5_01_M00930_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.69274e-06
E-value	0.00786549
q-value	0.00183772
Overlap	10
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Pou2f2_3748.1_Cell08_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.81234e-06
E-value	0.00821484
q-value	0.00183772
Overlap	10
Offset	3
Orientation	Normal

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Summary

Alignment

Name	Pou2f3_3986.2_Cell08_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.81234e-06
E-value	0.00821484
q-value	0.00183772
Overlap	10
Offset	3
Orientation	Normal

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Summary

Alignment

Name	OCT2_01_M01368_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.16464e-06
E-value	0.00924393
q-value	0.00183772
Overlap	10
Offset	3
Orientation	Normal

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Summary

Alignment

Name	POU2F3_01_M01476_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.16464e-06
E-value	0.00924393
q-value	0.00183772
Overlap	10
Offset	3
Orientation	Normal

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Summary

Alignment

Name	OCT1_05_M00161_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.01865e-06
E-value	0.0117385
q-value	0.0021215
Overlap	10
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	OCT1_Q6_M00195_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.17764e-05
E-value	0.0343989
q-value	0.00569884
Overlap	10
Offset	3
Orientation	Normal

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Summary

Alignment

Name	NFIX_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.29441e-05
E-value	0.0378098
q-value	0.00578209
Overlap	6
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	Tcfap2e_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.0955e-06
E-value	0.00612097
q-value	0.00764936
Overlap	9
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	AP2ALPHA_03_M01047_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.92933e-06
E-value	0.0114776
q-value	0.00764936
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	CBF1_02_M01699_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.12181e-06
E-value	0.00619781
q-value	0.0119025
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Mycn_MA0104.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.1223e-05
E-value	0.0327824
q-value	0.0184852
Overlap	6
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Arnt_MA0004.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.62266e-05
E-value	0.0473979
q-value	0.0184852
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	FRA1_Q5_M01267_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.6233e-09
E-value	1.05837e-05
q-value	2.10333e-05
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	BACH2_01_M00490_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.2499e-08
E-value	9.49294e-05
q-value	9.43286e-05
Overlap	9
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q4_01_M00926_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.60462e-07
E-value	0.00046871
q-value	0.000310495
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q6_01_M00925_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.4042e-07
E-value	0.000702266
q-value	0.000348911
Overlap	9
Offset	0
Orientation	Normal

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Summary

Alignment

Name	GCN4_01_M00038_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.2092e-07
E-value	0.00122951
q-value	0.000450769
Overlap	9
Offset	9
Orientation	Normal

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Summary

Alignment

Name	AP1_Q6_M00174_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.65909e-07
E-value	0.00136092
q-value	0.000450769
Overlap	9
Offset	1
Orientation	Normal

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Summary

Alignment

Name	AP1_01_M00517_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.20138e-06
E-value	0.00350924
q-value	0.000996295
Overlap	9
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_C_M00199_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.78345e-06
E-value	0.00520947
q-value	0.00125244
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_MA0099.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.94175e-06
E-value	0.00567186
q-value	0.00125244
Overlap	7
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	BACH1_01_M00495_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.50513e-06
E-value	0.00731747
q-value	0.00136468
Overlap	9
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	NRF2_Q4_M00821_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.58595e-06
E-value	0.00755356
q-value	0.00136468
Overlap	9
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_Q2_M01713_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.0568e-06
E-value	0.00892891
q-value	0.00147873
Overlap	9
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_02_M01555_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.60687e-06
E-value	0.0163777
q-value	0.00206203
Overlap	9
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_MA0303.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.60687e-06
E-value	0.0163777
q-value	0.00206203
Overlap	9
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	Gcn4_GR09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.60687e-06
E-value	0.0163777
q-value	0.00206203
Overlap	9
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	MAF_Q6_01_M00983_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.68344e-06
E-value	0.0166013
q-value	0.00206203
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Jundm2_secondary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.26469e-05
E-value	0.0369417
q-value	0.00407866
Overlap	9
Offset	4
Orientation	Normal

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Summary

Alignment

Name	Fos_MA0099.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.61615e-05
E-value	0.0472077
q-value	0.00469089
Overlap	8
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	RPS10_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.55759e-06
E-value	0.0133127
q-value	0.019628
Overlap	6
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	ZNF655_8_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.28948e-06
E-value	0.0212926
q-value	0.019628
Overlap	6
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	CBX7_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.35765e-05
E-value	0.039657
q-value	0.019628
Overlap	6
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	NUP133_3_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.35765e-05
E-value	0.039657
q-value	0.019628
Overlap	6
Offset	-2
Orientation	Normal

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The TOMTOM results consist of

The query motifs with links to further information on matches. [View]
The target databases with information on the number of matches. [View]
The matches between query motifs and target motifs. [View]
- The summary of match information.
- An alignment of the two motifs.
The program details including:
1. The version of TOMTOM and the date it was released. [View]
2. The reference to cite if you use TOMTOM in your research. [View]
3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
This explanation of how to interpret TOMTOM results.

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name: The motif name.
Alt. Name: The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website: A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview: The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches: The number of significant matches.
List: Links to the first 20 matches

Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database: The database name.
Number of Motifs: The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched: The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name: The name of the matched motif.
Alt. Name: The alternative name of the matched motif.
p-value: The probability that the match occurred by random chance according to the null model.
E-value: The expected number of false positives in the matches up to this point.
q-value: The minimum False Discovery Rate required to include the match.
Overlap: The number of letters that overlaped in the optimal alignment.
Offset: The offset of the query motif to the matched motif in the optimal alignment.
Orientation: The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.

Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type: Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars: Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC: Toggle adding pseudocounts for Small Sample Correction.
Flip: Toggle a full reverse complement of the alignment.
Width: Specify the width of the generated motif.
Height: Specify the height of the generated motif.

Query Motifs

Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: 1_e_k4me1-h1_0.558

Summary

Alignment

Summary

Alignment

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Alignment

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Alignment

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Alignment

Matches to Query: 2_e_k4me1-tro_0.552

Summary

Alignment

Summary

Alignment

Matches to Query: 3_e_k4me1-h1_0.541

Matches to Query: 4_e_k4me1-tro_0.538

Matches to Query: 5_e_k4me1-h1_0.536

Matches to Query: 6_h_k4me1-tro_0.535

Matches to Query: 7_e_k4me1-tro_0.534

Matches to Query: 8_e_k4me1-tro_0.534

Matches to Query: 9_e_k4me1-tro_0.534

Matches to Query: 10_e_k4me1-tro_0.533

Matches to Query: 11_e_k4me1-h1_0.533

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 12_e_k4me1-tro_0.529

Matches to Query: 13_e_k4me1-tro_0.528

Summary

Alignment

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Alignment